Cherry Blossoms
by AikoTsuki
Summary: The Ultimatum Project, an experiment in creating the perfect human. An experimet the Black Organiztion is interested in, one that Conan and KID find themselves involved in. COMPLETE
1. Prologue

**I don't own Detective Conan. **

**This story begins after episode 621**

* * *

**Prologue**

Conan was walking up to Agasa's house when he noticed two girls standing in front of his house. One was about Ran's age, with short dark brown hair and a calm, confident demeanor. The other was about 12 or so, with incredibly long pale pink hair and a cheerful, energetic expression.

"Hello, Kudo Shinichi."

Conan spun around. A teenage boy with light brown hair was looking down at him.

"I-I'm not Shinchi-niichan!" Conan stammered.

"Don't lie to me. You can't mess with a DNA test."

"Who are you?"

* * *

Ten minutes later, Conan, the boy, and the two girls were in the Kudos' study. The boy was Nakamura Tsukiya, and the girls were sisters: Tanaka Sakura and Hotaru. Hotaru was the older sister, and seemed to be pretty close to Tsukiya as she dropped the honorifics with the boy. They all seemed to be from the Kansai regin, all though Hotaru was a lot more formal than Heji was.

"How did you know about me?" Conan asked.

Hotaru flashed an INTERPOL badge."We were assigned to the Black Organization case. One of our contacts seemed to think you were trying to take down the Organization."

"Oh. So, um, where are you guys staying?"

Hotaru shrugged. "We haven't found a place just yet."

"Would you like to stay here?"

* * *

**Okay, I know Conan was ****_pretty _****trusting, but remember how he was with Okiya? **

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	2. Laundry Day

**This chapter is mostly filler, at least until the end.**

**I don't own Detective Conan.**

* * *

**Laundry Day**

Three weeks later, Conan and Ran walked over to the Kudo residence. Hotaru agreed to help Ran with her English assignment, and she decided to drag Conan along with her.

Sakura flung open the door. "Hi Conan-kun! Hi, Ran-neesan!" She led them inside. "Neechan says you'll have to wait until we finish doing the laundry for her to help you with your assignment."

"Can we help?" Ran asked.

"Sure." Tsukiya walked in carrying a basket of laundry. "We're just hanging everything outside to dry, so it won't take long."

A few minutes later, Ran noticed the large load of laundry. "I didn't think you all went through clothes _that _fast," she commented.

Hotaru hung a sheet on the clothesline. "We don't. Most of it is the linens. I don't think anyone's washed them in ages."

Tsukiya ran outside with another basket, tripped, and fell onto the grass, spilling clothes everywhere.

"Tsukiya!"

* * *

She stared at the DNA analysis. _Two of the missing experiments, _she thought. _But are they the ones we need?_

There were four missing experiments from the project, which ended eight years ago. But these had been missing for sixteen years. Hopefully, one of these would be one of the twins. That person wanted the twins. Although, another experiment would be usefull as well.

She handed a file to Gin. "The boss wants you to bring these two to me. Alive."

* * *

Laundry done, Hotaru and Ran sat down to work on Ran's assignment. "Ran, I was wondering if your dad would be willing to help my parents with something."

"WHat is it?"

"You see, my stepfather has this valuable choker necklace that's been in the family for almost a thousand years. Yesterday, he recived a note from KID saying he was going to steal the necklace at midnight during a party my parents are throwing in Kyoto."

"When's the party?"

"In one week."

* * *

**Okay, maybe it's a little more than _just _filler.**

**Please read and review!**


	3. Converging Lines

**Thanks for your reviews!**

**Abe Lincoln Lover: Thanks for your suggestions. I like long chapters as well, so there will probably be a mix of both, depending on what's happening in the chapter.**

**I could imagine whis being its' own show. Now what would be cool. But, what would the opening and closing be? I'll have to think about that**

**Disclaimer: I don't own Detective Conan**

* * *

**Converging Lines**

Hotaru, Sakura, Tsukiya, Conan, Ran, and Kogoro stepped off the plane. Hotaru explained earlier that the party was to celebrate the start of the sakura-viewing season, and many wealthy businessmen and their families wold be attending. The Detective Boys would be attending, along with Heji and Kazuha.

Hotaru scaned the airport."Where is he?" she muttered.

"Who are ya lookin' for?" Kazuha asked.

"My brother. He promised to pick us up."

A teenage boy ran up with a first-grader following close behind. "Sorry we're late," the teen apologized.

Hotaru shrugee. "It's okay. We just got here." She turned to the group. "Everyone, this is Ichirou, my twin, and Masahiro, my half-brother."

* * *

Hakuba walked up to the front desk. Kaito was there, cheking into his room.

"Kuroba? What are you doing here?"

Kaito picked up his room key. "Me? I'm here to see this hotel's sakura garden. What about you?"

"I was asked to help catch KID at his heist tonight."

Kaito started to walk away. "Good luck!"

* * *

"_That's _the necklace?" Kazuha asked. "It's beautiful!"

The choker was several rows of pink freshwater pearls offset by a large heart-shaped ruby pendant.

"I can see why KID would want to steal it," Ran commented. "It must be worth a lot of money."

Hotaru's mother, Kiomizu Rina, nodded, touching the pendant. She would be wearing it during the party. While Mrs. Kiomizu gave the group of the 5-star hotel they were staying at- and the Kiomizus owned- Tsukiya left to oversee party preparations and Hotaru walked into the sakura garden.

She sat on a bench by a small, mirror-like pond. The party would be starting in a half hour, but she was already ready.

She looked around. "A lot can change in ten years," she whispered. Looking into the pond, she was flooded by painful memories.

Oton often played with her by this pond, at least until he died of leukemia shortly after Sakura was born. He died on that very same day as today, twelve years ago. Okan remarried only a year later. Didn't she care about Oton?! An angry tear slid down her cheek. She started crying silently, tears dripping into the pond.

Suddenly, a bouquet of white roses appeared under her nose. She looked up at the boy holding it out to her. He smiled. "I don't like seeing a pretty girl like you cry."

"Okini." She breathed the bouquet's sweet scent. "What's your name?"

"Kuroba Kaito."

"Tanaka Hotaru."

* * *

**Yay! All the people are starting to meet each other! Now for the fun part!**

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	4. Dance

**Dance**

Kaito looked at his watch. He had six hours until the heist, giving him plenty of time to spend with Hotaru. The party had already started inside the hotel, but no one knew about this spot. Sad, really, it was the perfect spot if you were planning something romantic the perfect view of the stars, the cherry trees in full bloom, the mirror-like pond with a bench sitting next to it.

"Why don't I go inside and get us something to eat?" Kaito suggested. They'd been talking for a while now, and he was starting to feel hungry.

"Sure."

Kaito walked inside, grinning. Hakuba noticed him. "What's got you so happy?"

"I met someone."

Aoko and Hakuba started dating a month ago, leaving Kaito heartbroken. Maybe he could start fresh with Hotaru, she seemed to like him.

He returned to the bench. "By the way, why were you crying? Did your boyfriend break up with you or something?"

"No. It's because today is the 12th aniversary of my father's death."

"Oh. I'm sorry. My dad died when I was eight."

They talked for a long time, exchanging shildhood experiences, and Kaito showed Hotaru some magic tricks, which she loved. A song floated to them from inside.

Kaito stood up and bowed. He smiled. "May I have this dance?"

* * *

Conan was incredibly bored. The kids were playing childish party games. He and Haibara hung around near the back, watching everyone else.

Conan noticed Ran standing by herself along the wall. She looked sad. Kazuha and Heji wre dancing together, and Kogoro was flirting with some woman. Tsukiya and Ichirou were part of security, and Hotaru vanished ages ago. He wished he could be with her, as _Shinichi._

Haibara handed him a pill. "Here."

"Is this-"

She nodded.

Conan ran off. "Domo!"

* * *

Ran stared off into space. If only Shinichi or Hotaru or _someone _were her, so she wouldn't be alone.

She heard footsteps. She looked up. Shinichi was standing in front of her, smiling nervously.

"May I have this dance?

* * *

**Okay, this chapter was moslty setting up for the next one. **

**Please read and review!**


	5. Countdown

**Here's where things start to get interesting.**

**I think I figured out what I'd want the opening and closing to be: the openig would be "Again," by YUI, and the closing would be "Haunted," by Evanescence.**

**I don't own Detective Conan.**

* * *

**Countdown**

_**Play Going Under- Evanescence**_

11 o'clock. One hour until the heist. Kaito's fairytale evening would have to end.

He stood. "I have to leave."

Hotaru stood as well, long turquise tulle skirt swishing in the gentle spring breeze. She nodded. "Good luck, Kaito-kun."

* * *

She looked at the video feed from the cameras placed throughout the ballroom.

"Both targets are in place," an agent reported.

Her eyes narrowed. That boy, he looked just like Target A, only he wasn't. Could he be the other twin?

She tapped the boy's image. "Drop Target B. Go for this one instead."

* * *

Hakuba stood by the necklace, which was in a glass case on the stage.

_Only a half hour until the heist._

* * *

Ichirou leaned against the wall, scanning for any possible threats. He didn't notice his sister standing next to him.

"How are things going?"

He looked over. That strapless, low-neckline dress was something Hotaru would _never _wear, unless okan made her. And yet, the onyx necklace and matching earrings oton bought for her 15th birthday matched it perfectly. He grinned. "Everything's fine. You look great, by the way."

She rolled her eyes and sighed. "I found them, Ichirou."

"Who?"

_"The twins."_

"Oh, them. Where are they?"

She gestured at a figure on the dance floor. "But the other seems to have vanished."

* * *

She started the countdown.

_10...9..._

Smoke filled the stage.

_8...7..._

A figure appeared on the glass case. Kaitou KID. He stood.

_6...5..._

"Hello, everyone!"

_4...3..._

Two shots pierced KID's body.

_2...1..._

The lights went out, precisely on cue.

* * *

**Yay! Now things are starting to get interesting!**

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	6. Capture

**Abe Lincoln Lover: I'm happy you're enjoying my story. I'll tell you right now, KID goes a bit nuts in the next chapter, but only then. Yeah, he and Hotaru are going to start a relationship.**

**I don't own Detective Conan.**

* * *

**Capture**

_**Play Hero- Breaking Benjamin**_

Hotaru put her hand on her friend's shoulder. "Don't worry, we'll find him."

Ichirou told security to keep an eye out for Shinichi. Hotaru pulled him aside. "I have a bad feeling about this," she said.

Ichirou nodded. "Do you think it could be Them?"

Tsukiya ran up. "One of the guests saw a man in black carry Shinichi-han outside!"

* * *

A bright light was shining in Shinichi's face. He squinted, trying to turn his head away from the light.

"Oh good, you're awake."

Shinichi tried to sit up. His wrists and ankles were tied to what felt like a metal tables. A figure hovered over him. It looked like...a woman?

"I am Merlot, and I'm about to have some fun with you."

* * *

They questioned the guest and Ran. It looked like the captor- a member of the Organization- took advantage of the pandemonium and used it to knock out and kidnap Shinichi, then carry him outside, claiming the boy needed some fresh air.

Hattori came over, having heard the situation.

"Is there anything I can do to help?"

Ichirou shrugged.

"Why would they kidnap Shinichi?" Ran asked.

"Because, Shinichi's not an ordinary human," Hotaru said.

* * *

Kaito opened his eyes. "How about you let us go? That would be fun."

Merlot shook her head. "I'm not about to let such _valuable _experiments go."

"Experiments?" Shinchi asked, sounding as confused as Kaito was.

Merlot smiled. "So you _don't _know. Excellent."

Merlot and her assistant plunged a needle into Kaito and Shinichi's arms.

* * *

"What do you mean?" Heji asked.

Hotaru sighed. "About twenty years ago, a group of American and Japanese scientists began an experiment known as the Ultimatum Project. They were trying to create a perfect human being."

Ichirou nodded. "They started by enhancing thier experiments' strength, agility, speed, and intelligence in the womb. After being born, the children went through a series of drug therapies and experiments, giving them rather _unusual _abilities."

"Was Shinichi a part of this?" Ran asked.

"We believe so. About 12 years ago, four experiments vanished from the lab, along with several doses of Metaphen," Tsukiya replied.

"What's that?"

"A drug used to change your appearance," Hotaru explained. "It also suppresses genetic enhancements."

"How do you know Kudo's an experiment?" Heji asked.

"We found traces of Metaphen in his system, along with supressed genetic enhancements."

* * *

Kaito moaned with pain. He felt like his body was melting, like his brain was boiling. His skull felt llike it was about to explode.

"What did you...do to me?" he gasped.

Merlot leaned close and smiled. "I'm helping you realize your full potential," she whispered.

Kaito's world went black.

* * *

**What's happening to the boys? Why does Hotaru know so much about the Ultimatum Project? Keep reading!**

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	7. Control

**I don't own Detective Conan**

* * *

**Control**

_**Play Lose Control- Evanescence**_

Ran and the others went upstairs to chnage, agreeing to meet back in Hotaru's romm. When Ran walked into her friend's room, Hotaru was on her laptop.

"What are you doing?"

Hotaru looked up. "Ultimatum experiments release a special pheremone, which I'm looking for since Shinichi-han's captors likely gave him Zeta."

"Zeta?"

"It's a drug that undoes the effects of Metaphen. Once he's back to normal, his pheremone signature should be visible. Ah, here it is." Hotaru cliked her mouspad a few times. "I have his location."

By now, the others had arrived.

"Let's go," Tsukiya said.

* * *

Kaito opened his eyes. He felt..powerful. It felt amazing. He looked at his wrists, which were restrained by plastic ties. He snapped them like they were made of wet paper.

He got off the table. "Shinichi-san, wake up. We're alone."

A figure stirred. "Wha's going on?"

"Shinichi-san, is that you? You look...different."

"Different _how?"_

"Um, your skin is paler, and your hair is blond and kind of spikey. And your eyes are turqoise."

"I could say the same about you," Shinichi said.

"Really? Cool."

"How did you escape?"

"I broke my restraints. Merlot made us a lot stronger, you should try to get free, too."

Shinichi broke free of his restraints. He sat on the table, rubbing his wrists.

Merlot walked into the room. "Don't you dare try and escape. Come with me, quietly, and you won't be harmed."

Kaito grinned. "Make me."

* * *

They made their way downstairs to the car. The police would be useless, or so Hotaru said. Shinichi would simply be moved to another location.

It amazed Ran that Hotaru could walk in a straight line while monitoring her computer screen without walking into anything. Something was bothering Ran. "Hotaru-chan?"

"Yeah?"

"Why do you know so much about the Ultimatum Project?"

Hotaru stopped. "Oh, _that._" She sighed. "It's because Sakura-chan and Ichirou were experiments in the Project."

"_Were _experiments?"

Tsukiya nodded. "Six years ago, INTERPOL found out about the Project. They managed to arrest the scientists involved and free the experiments. Sakura-chan and Ichirou-kun were some of the few who manages to find their families."

"Oh."

Hotaru sighed. "After a while, a number of experiments and concerned individuals joined together to form the Mutant Protection Comittee, which works to keep the experiments safe."

"Are you a part of it?"

"My parents _run _the Comittee."

* * *

Kaito was out of control. The guards tried to restrain him, but he was too strong and fast. Bullets couldn't stop him, tasers didn't even faze him.

"Calm down!" Shinichi shouted.

"Why are you taking their side?!"

Kaito reminded Shinichi of a bull in a china shop, injuring guards as well as himself, destroying instruments and equipment, crashing into walls.

_He's going to hurt himself._

With similar speed and strength, Shinichi grabbed Kaito and held him down.

"Let me go!" Kaito shouted, struggling beneath him.

"Not until you calm down!"

"Thank you, 171," Merlot said. "You have far better control than your twin."

"Twin?"

A needle plunged into Kaito's arm, and he passed out. A similar thing happened to Shinichi.

* * *

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	8. Missing

**Thanks for reading! Sorry for not updating in a while, I had a serious case of writer's block. But I found my muse, and here we go!**

**Conan02: Don't worry, just keep up with this. The reason Kaito flipped out is about to be explained.**

**I don't own Detective Conan.**

* * *

**Revelation  
_Play Headstrong- Breaking Benjamin_**

Merlot opened her laptop and began typing her report.

_Project Awakening has been a sucess. EXP 170 and 171's abilities are far greater than expected. Psychic ablilities have been activated. EXP 170 is experiencing a hypersenistivity to adrenaline. Requesting Trithydrine, may decrease hormone sensitivity. Considering APTX 4869, 98% chance of reducing EXP age by 5 yrs, giving more time to learn to control abilities. Requesting assistance in convincing EXPs to cooperate._

* * *

The car ride was quiet. The only person who said anything was Hotaru, who was giving Heji directions.

"Oh no."

"What is it?" Heji asked.

"Shinichi-han's signal...it vanished."

"Where was it?" Ran asked.

"An abandoned laboratory about 5 miles from here."

"We'll check there first."

* * *

Merlot glanced at the boys. 171 had been previously given APTX, but Zeta eliminated the effects of that. She was to give both experiments a dose of APTX and Trithydrine, then she, Noir, and Gin were to take them to a safe house in teh Okachichibu Mountains.

Merlot shook her head. Gin was there for security purposes, but he wasn't very good with children, so why was _he _coming? Then again, Noir was good with kids _and _keeping Gin under control, so she supposed everything would be fine.

She prepared a syringe for both boys. She began with 170, then his brother.

The transformation took about ten minutes. Noir was busy getting the boys fitting clothes and arranging a helicopter to take them to the safe house.

Merlot pulled out her cell and texted the Boss. _The experiments are ready._

* * *

After 20 minutes of Heji's crazy driving they arrived at the laboratory. It looked like it hadn't been used in at least a decade.

They split into two groups- Hotaru and Ran, and Ichirou, Tsukiya and Heji.

Ran and Hotaru walked into a room. There were recently-used machines, along with partly-used bottles of APTX, Zeta, and Trithydrine.

"They were here, but not any more."

* * *

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	9. Transportation

**I don't own Detective Conan**

* * *

**Transportation**

Noir looked out the window at the mountains below. She'd never been in this part of Japan before.

Gin was in front with the pilot. The twins were in the back, with Noir on one side and Merlot on the other.

Merlot hadn't been too happy about being sent to the middle of nowhere. Noir agreed with Gin, you had to comprimise convenience for security.

Noir wasn't like the other members of the Organization. First of all, she was a ninja, which was why she didn't have to wear a black trench coat and fedora. (It impeded her movements.) Secondly, she was an experiment in the Ultimatum Project- EXP96.

Noir was very loyal to the Organization. They'd given her a palce in the world, a fresh start, a life. She'd do anything to herl them succeed.

* * *

They regrouped outside.

"This place was regrouped recently," Heji said. "They can't be too far away."

Ichirou shook his head, "What if they took a helicopter? Even if they left by car, they could still be anywhere in Kyoto."

Ran was distraught. The poor girl had basically learned all of Shinichi's secrets in the past hour- even the ones he wasn't aware of- and now it looked like she might never see him again.

Tsukiya raised his haid. "One question- do we know exactly who took him?"

"The people who created APTZ 4869- the Black Organization."

* * *

They arrived at the safe house- a mansion in the woods, miles away from a town or even a hiking trail.

Gin disappeared as soon as they arrived, leavign the girls to carry the twins inside. The boys would be unconscious for at least another hour, that's what Merlot siad.

"Did the Boss give you any instructions?" Merlot asked.

Noir nodded. "I'm supposed to alter their memories, make them believe they reccently escaped the lab a few months ago, that they really are twelve, give them new names."

"They might be more cooperative if they see this place as a safe haven," Noir agreed.

They put the boys in their beds. "Let's get started, then."

* * *

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	10. Awakening

**Once again, I apologize for the break in chapters. I was on a bit of a roll, until I lost my muse.**

**Conan02: Thanks for the correction. I'm just happy I got the 4869 correct.**

**I don't own Detective Conan, but I do own Noir, Merlot, Tsukiya, Sakura, Ichirou, and Hotaru**

* * *

Ran looked out the window during the flight back to Tokyo. Hotaru believed that Shinichi was still in Japan, but he could be anywhere. She downloaded a program to find specific genetic codes (ie Shinichi's), but locating Shinichi could take anywhere from a few hours to a few weeks.

She had some questions she wanted answered who rescued Shinichi, twelve years ago? Where are they? How did the Kudous get ahold of him? Did they know? Sadly, no one in the group could answer these questions. The only way to find out was to unlock Shinichi's repressed memories, which would be an incredibly painful experience. But they had to find him before they could do anything.

Hotaru leaned over. "I'm getting close."

Ran smiled.

* * *

Hajime (ie Shinichi) opened his eyes. He wasn't in the lab, so where was he?

He was in something...comfortable. A bed?

He sat up. Someone had given him a pair of pajamas. Kyou (Kaito) was in the bed next to him. He crawled over and shook Kyou's shoulders.

"Wake up, Kyou!" he hissed. "Where are we?"

Kyou sat up, rubbing his eyes. "Wha?" He looked around. "We're not in the lab. I think we're in someone's house."

"How did we get here?" Hajime asked.

"I don't know."

They opened the curtains. They were in a wooded valley, the building set in a large, open clearing.

The door opened. Both boys tensed, preparing to defend themselves.

A girl walked in. She was maybe 17 or 18, with long midnight-blue hair. She smiled. "Glad to see both of you are awake."

"Where are we?" Kyou asked.

"A safe house in the mountains. My name's Noir."

* * *

They stepped off the plane. Heji and Kazuha had gone back to Osaka, and Ichirou and Sakura were staying in Kyoto, so the group now consisted of Tsukiya, Hotaru, and Ran.

"Shinichi-han's somewhere in the Okachichibu Mountains," Hotaru said. "It'll take me a while to pinpoint his _exact _location."

* * *

Merlot wrapped up her report. She had just finished testing the twins' abilities. 170 could heal, and read auras and minds. 170 could see the future and generate fire and force fields. Due to the Link, both twins could communicate telapathically, and each was aware of what the other twin was experiencing. They had little to no control over their ablilities, but with a little work...

She took a second glance at their readings. "Amazing," she whispered. "Their power is simply incredible."

The Boss would be pleased.

* * *

"Look at this!"

"Come over here, Kyou!"

Noir smiled. After Noir finished testing the twins they were allowed to explore the mansion. It _was _pretty big- 36 bedrooms on 4 floors, with a library, pool, game room, movie theater, weapons vault, and training area. Then again, it did beslong to the Boss as one of his vacation homes.

Security personnel and staff would be steadily increasing over the next few weeks in preparation for the Boss's arrival in two months. Noir just hoped she could get the twins ready in time. After all, they were being prepped to take over the world.

* * *

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	11. Movements

**Sorry for the break in updates, been working on four fanfics at once.**

**But now I have time to work on this one.**

**Disclaimer: I don't own Detective Conan.**

* * *

_**(Play Wanted- Vanessa Carlton)**_

One week passed. Aoko was worried about Kaito. So was Hakuba, even though he wouldn't admit it. So the two decided to go to the Mouri Detective Agency for help.

"Sorry, Detective Mouri's not here right now," Heji said. "But I'll take a look if you want." He was in Tokyo to help with the search, supposedly.

Aoko handed the photo. Heji's eyes widened. "Ran-chan, Hotaru-chan, you might want to take a look at this!"

Both girls came downstairs. Heji handed them the photo.

"He looks just like-" Ran started to say. Hotaru nodded. "I'll put him on my list."

"Who does Kaito look like? What list?"

The three looked at each other.

* * *

Noir looked out the window. The twins were playing soccer outside. Of course, their powers were involved, making the game incredibly entertaining to watch.

Noir was glad the Boss was sending the staff slowly to allow the boys- especially Kyou- to adjust to new people. Too many minds would be dangerous, at least until Kyou learned to filter thoughts.

She'd only heard rumors about the Boss's master plan. The only part she knew for certain was that he needed the twins. But for what?

* * *

Hotaru had been running an analysis of Kaito's DNA while Ran explained the current situation to Aoko and Hakuba.

Hotaru looked up from her laptop. "Yep, he's Shinichi-han's twin. Wait a second..." She looked back at the screen and started typing furiously.

"What is it?" Ran asked.

"It says ther at two experiments in the room, but Tsukiya and Ichirou are in Hong Kong-"

"Then who are they?" Heji asked.

"Ran-chan and Aoko-han."

* * *

**~Please read and review!~**


	12. Transformation

**Just warning you, the twins are going to be out of the story for a chapter or two, so no complaining!**

**I don't own Detective Conan.**

* * *

**(play Koi wa Suriru, Shokku, Sasupensu- Rina Aiuchi)**

"What do you mean, are Ran-chan and Aoko-han experiments?" Heji demanded.

Hotaru didn't hear him, she was busy analyzing their DNA. "So they _are _the other missing experiments," she muttered.

"What do you mean?" Hakuba asked.

Hotaru didn't look up. "The twins weren't the only ones to escape. A total of four expiriments vanished from the lab."

"So Aoko-san and I are-"

"The other missing experiments."

_One week later_

Everyone met up at the Kudo residence. Ran and Aoko were going to take Zeta, and Hotaru wanted to wait until Ichirou and Tsukiya came back. They were the experts on the drug, after all.

"Okay, you can take either the quik-acting or the long-release version," Ichirou explained. "The quick-acting is dangerous and excruciatingly painful, but it only takes 15 minutes. The long-release is safer and you're unconscious most of the time, but it takes 24 hours."

Both girls picked the long-acting version. Ichirou and Tsukiya each filled a hypodermic needle with a precise amount of a pale blue liquid and injected it into a girl's arm.

Aoko and Ran passed out almost instanly.

The next 24 hours were spent helping the girls through the transition. Agasa, Haibara, Heji, and Ichirou helped Ran; and Hotaru, Hakuba, and Tsukiya took care of Aoko.

The girls shifted in and out of consciousness, delerious and feverish. Hakub had to wonder how much worse the quick-acting Zeta would have been.

Finally, the fever went down. Ran and Aoko went to wash their faces, knowing they'd look diferent.

They were right. Both girls now had super-log, straight black hair. Ran had short bangs and her eyes were violet. Aoko's bangs were longer, and her eyes were green.

"Fraternal twins," Hotaru noted. "Wonder why I didn't pick up on it earlier."

"What's so special about twins?" Hakuba asked.

"Twins in the Ultimatum Project were naturally psychic, and any genetic changes were more pronounced, more so in identical twins like Kaito-han and Shinichi-han. However, their psychic abiliteis could not be activated until they touched each other."

* * *

**Please read and review!**


	13. Remembrance

**Okay, here's where some things about the past are about to be explained.**

**I don't own Detective Conan**

* * *

**(Play START- Rina Auichi)**

Hotaru expected to find Kaito and Shinichi within the next few days. In the meantime, she and Ichirou were going to train Ran and Aoko, after they found out the girls' powers, and helped them remember the memories they'd repressed from while they were in the lab.

Aoko and Ran took the train to the MPC's Tokyo headquarters, which was in the Tokyo Bay area.

"I think we should change our names," Aoko said. "After all, I'm no more Nakamori Aoko than you are.:

Ran looked out the window. "I want to wait until we're finished with the Organization."

Aoko shrugged. "Well, I'm going to talk to Ichirou about it."

The MPC building was huge, since it also housed Tanaka Industries, the company Hotaru's parents ran and used to fund the MPC's activities.

The top half of the 46-floor building was for the MPC. The testing center was on the 30th floor.

Hotaru and Ichirou were waiting for them. Hotaru led Ran into one room, Ichirou led Aoko into another.

Hotaru took Ran to a plain white room. The only things in the room were a chair and an MRI-type machine.

Ran sat on the patient table. "What do I do?"

Hotaru handed her a pill and a glass of water. "Take this, then lie down and try to relax."

Ran obeyed. She felt a slow, rhythmic pulse. The inside of the machine glowed softly, quickly getting brighter. She closed her eyes.

_Ran opened her eyes. She was in a room in a laboratory. Scientists in white lab coats ran around outside, moving with urgency and purpose._

_A little girl- maybe five years old- was strapped to a chair, struggling uselessly. One of the scientists in the room injected her with something._

_The girl writhed and screamed in pain. She eventually calmed, her brown eyes now violet._

_The scientist turned to his partner. "Another success!"_

_The woman nodded, pressing a cloth to his face. The scientist passed out._

_The woman walked up to the girl and undid her restraints. "Come with me."_

_The woman led the girl through the brightly-lit, hospital-like halls to the outside. The building they came from was surrounded on all sides by a tall brick wall topped with barbed wire,_

_Another scientist walked up to them, leading a pair of blond-haired twin boys. "So far so good," he whispered._

_The group approached the gate. "Hey! You can't take experiments outside the compound!"_

_A woman knocked out the guard. The gate opened. "Let's go."_

_They ran to a van hidden in the woods. The adults took off their disguises. The two "scientists" were Mr. and Mrs. Kudo. Ran didn't recognize the other woman._

_The three children were going to live in Japan as ordinary human beings. They wouldn't remember anything. One of the twins would become Kudo Shinichi, the other Kuroba Kaito. The girl became Mouri Ran._

* * *

_Aoko had a harder time. It was another hellish 18 months before she was rescued._

_All the lights went off in the building. Some of the other experiments around her were panicking._

_Someone opened the door of Aoko's cage. "Come on out," a woman said. "I won't hurt you, I promise."_

_Aoko crawled out hesitantly. The woman led her through eerie halls dimly lit by emergency lights._

_Outside, the building was pitch-black. They ran towards the locked gate. The woman aimed a remote-like device at the gate and it opened. _

_The woman led Aoko into the woods. When they were safe, the woman held her close. "I'm so glad you're safe, Midori," she whispered. _

_"Who are you?"_

_"I'm your mother, Aoi Kyomi."  
_

Aoko opened her eyes. _Kaasan. _The woman looked like an older version of her, with short hair. Some day, Aoko would find her.

She sat up. Ichirou was watching her. "You wanted to change your name?"

Aoko nodded. "I'm not Nakamori-keibu's daughter."

"So then who are you."

"Aoi Midori."

* * *

**The twins return in the next chapter!**

**Please read and review!**


	14. Escape

**The twins return! Spoiler alert: Plot twist ahead!**

**I don't own Detective Conan.**

* * *

**(Play Into the Fire- Sarah Mclachlan)**

Noir leaned against a tree trunk. All this time, she trusted them, _helped _them. But she wasn't truly free, they'd always been experimenting on her- and the twins- and she'd never known.

But they wouldn't do this, not any more. She'd make sure of it.

* * *

Midori, Ran, Ichirou, and Hotaru got together to discuss what the girls had seen in their memories. They finished hearing from Ran when Hotaru's phone started to ring. She stood. "I'll be right back."

Hotaru stepped into the empty hall and answered her phone. "What's up?"

_"It's been a while, Tanaka."_

"Noir?" Her voice quieted. "What's going on? Why are you calling me _now_?"

_"They've been experimenting on us."_

"'Us?'"

_"Me and the twins. I assume you're looking for them?"_

"Where are you?"

_"I'll tell you if you help me and the twins escape."_

"What do you need?"

* * *

_One week later _

Noir looked at the clock.

_3...2...1..._

At precisely 10 p.m, all the electricity in the safe house went off, exactly as planned.

Noir used her powers to create a double. The original picked up Hajime, and the other picked up Kyou. The boys were in a drugged sleep. Noir didn't have time to restore their memories, but didn't want them to make a fuss.

They ran towards the edge of the grounds, leaping over the fence. The alarm didn't go off. Perfect.

She had to find the cave she'd spotted on the way here. It wasn't more than a mile away, but it was nearly impossible to see in such a thick, dark forest.

* * *

**Please read and review!**


	15. Situation

**I can't believe I've written so much! The story has actually gone in a drastically different direction than I originally planned. **

**I'm past 5,000 words! Yay!**

**I don't own Detective Conan.**

* * *

**(play Koori no Ue ni Tatsu You Ni- Komatsu Miho)  
**

Hotaru looked at her phone. "Noir says they can't see anything. It's too dark."

Tsukiya stood. "I'll go. I have really good night vision."

Ichirou nodded. "Bring them back to the cave by dawn. We need to get out of here before they can send out a search party."

* * *

Noir (and her clone) sat on the ground. "Someone's coming to help."

"Who?"

"Tsukiya."

"Ah. That makes sense."

After a few minutes they heard an ATV approaching. Noir shielded her face from the headlight's glare. "Hop on," Tsukiya said.

* * *

Merlot looked at Gin. "We need to find them, quickly."

"I know."

She sighed.

"What is it?" Gin growled.

"My assistant accidentally gave 140 Ananimo. If we don't find him within the next 12 hours, we'll lose him.

* * *

Noir's clone noticed something was wrong with Kyou. His breathing was off, and his whole body felt hot.

She leaned over. "Something's wrong with Kyou-kun."

Tsukiya nodded. "We're almost there."

Over the past few weeks the twins had started to feel like little brothers. If anything happened to them...

She didn't want to think about it.

* * *

**Please read and review!**


	16. Time Limit

**Thanks for reading!**

**Detective2Conan: Of course there will be more! This story is almost done, but I am planning to create a sequel.**

**I don't own Detective Conan.**

* * *

**(Play Tourniquet- Evanescence)  
****_Hotaru's POV_**

Tsukiya drove up with Noir(s) and the twins.

"Something's wrong with Kyou," Noir said.

"Who?"

_"Kaito."_

I opened my laptop. "I'll need a blood sample."

Someone handed me a syringe with Kaito's blood. I poured a bit into the tray attached to my computer.

An alarm went off.

WARNING! ANAMINO DETECTED!

"Shit."

They all turned to look at me.

"Anamino."

"Ana- what?" Heji asked.

"A poison that causes the body to slowly destroy itself," I explained. "We have 12 hours."

I felt the muzzle of a pistol against my head,

"If I were a _real _enemy, you'd all be dead by now."

I turned. "Neechan!"

* * *

**_(Ichirou's POV)_**

Standing behing Hotaru was a 25-year-old blonde. Kaji, my older sister, who'd spent the past 3 years in Hong Kong.

Hotaru explained our situation to Kaji.

"12 hours, huh?" She looked at our small group of ATVs. "There's no way you'll make it to Tokyo in time on those."

Our faces fell.

"Thankfully, I have a chopper."

* * *

**YAY! I finally get to introduce Kaji! She's the one who taught Hotaru everything she knew- hacking, lockpicking, fighting, etc.**

**Please read and review!**


	17. Firefight

**I don't own Detective Conan.**

* * *

**play Unbreakable- Fireflight  
**"A helicopter was spotted a few miles from here!" an underling announced.

"In this remote area?" Gin asked. "That's who we're looking for."

* * *

**_Noir's POV_**

Kaji and Hakuba piloted the helicopter, while the rest of us sat in the back.

I turned to Hajime- err, Conan. "I'm going to restore his memories," I announced.

I closed my eyes and touched his forehead. I felt the barrier I created. I broke through. Then I felt an older barrier blocking his earliest memories. In order to wake him up, I shattered the second wall.

* * *

He checked the radar. "The experiments are one kilometer away," he announced.

Beside him, a woman leaned foreward, face focused and stern. "Don't kill them, just take down the helicopter."

The gunner nodded. That ice woman scared everyone. She was their boss's second-in-command, and she didn't get there by being nice.

She grinned. "Time to have some fun."

* * *

_**Ran's POV**_

Conan opened his eyes. He sat up. "Where am I?" An explosion outside shook the heicopter. I held him tight.

"What's going on back there?!" Kaji shouted.

I looked behind us. "Two choppers with big guns on our tail!"

"Are there any symbols?"

I checked. "Uh, yeah. One has a red firebird, the other's blank."

Kaji swore loudly. "Pheonix _and _the Organization?!"

"Who?" Midori asked.

"Pheonix is a group that wants to use mutants as a weapon to take over the world," Hotaru explained. "They funded the Ultimatum Project."

"And they're trying to kill us!" Ichirou shouted as another explosion shook us.

Kaji handed control of the heicopter to Hakubam then set up the machine gun and started firing.

We were over Tokyo a few minutes later. Kaji was scanning the ground. "Hover right here!" she ordered.

We were above a big pond. A missile was heading straight for us.

"Jump!"

* * *

**Please read and review!**


	18. Chasing Shadows

**My goal is to make it to 10,000 words. Or 20 chapters. I'm getting pretty close.**

**I don't own Detective Conan.**

* * *

**Play Haunted- Evanescence  
****_Hotaru's POV_**

I felt the wind rushing past me as I fell, closing my eyes. Above me the heicopter exploded.

PLOOSH!

I fell into the water. Some unseen force was pulling me down, deeper and deeper.

I landed on dry, solid ground. I stood as the others landed around me in the underground chamber.

"Why is this place so familiar?" I muttered.

Ran looked at me. "Hotaru? You look...different."

"What do you mean?"

Midori handed me her compact mirror. I gasped. My hair had gone from short and dark brown to shoulder-length and honey-colored. My eyes had gone from pale grey-blue to green-gold.

"What's going on?"

Kaji bowed. "Welcome to the Hall of Origins, Mistresses of the Sun and Moon."

* * *

10 minutes. Nothing. No bodies, no sign than anyone was there.

"They must have escaped," Gin said. "Search the area!"

* * *

She knew something was up. No one could hold their breath for _that long._

She was quite familiar with the old legend. Could this be the place?

* * *

**_Ran's POV_**

Something this place was very familiar, and the things Kaji said seemed to resonate with me.

I absentmindedly summoned a staff, as did Hotaru. Mine was gold, and at the top was a red crystal orb inside a gold sun. Hotaru's was silver with a blue crystal orb inside a crescent moon.

"Mistress of the Sun-" I whispered.

"And Moon," Hotaru finished.

Kaji nodded. "You are the caretakers of this place, the source of all magic- and life."

We heard a rumbling. "Shoot, they're coming," Kaji muttered. "We need to get to the Mirror Pool, there we can save Kyou."

We heard footsteps. "If they find the Pool, they'll misuse it, ane we'll all be doomed."

I had an idea, as I remembered a spell. "Why don't we use our Shadows as a distraction?"

Hotaru grinned. "Excellent."

* * *

Gin followed the woman into the tunnels. He emerged- alone- in a massive white hall.

He heard giggles. Shadows darted around the corner of his eyes. He chased after one.

* * *

**_Hotaru's POV_**

Shadows are illusions created to look just like someone. After creating Shadows out of me, Ran, Heji, Midori, Noir and Kaji, we took off.

Ran and I somehow knew where everything was in the Hall of Origins, so we led the way.

* * *

**Please read and review!**


	19. Confrontation

**I don't own Detective Conan**

* * *

**Play Book of Days- Enya  
****_Midori's POV_**

Hotaru wasn't the only one who's appearance changed. Noir and her clone now looked like two different people. One had short light brown hair, the other's was incdedibly long and blond. I mentioned this to them.

The blonde smiled. "That's because we _are _two different people. My name's Chiyoye."

"And I'm Amaterasu."

Chiyoye, Amaterasu, Kaji, Tsukiya and I were mages, apparantly, so we could see what our Shadows saw. Someone had ignored the illusions and was following us.

"Kaasan."

"Hmm?" Hotaru looked at me, confused.

"My mother...she's here."

"Who's your mother?"

"Aoi Kyomi."

Kaji shook her head. "Kyomi-san is Pheonix's second-in-command, and she's _not _your mother."

"She's coming," Chiyoye announced.

I waved them off. "I'll hold her off. You guys go ahead."

They vanished down the tunnel. Kyomi appeared.

"Hello, Midori."

"Kyomi-san."

She tilted her head, green eyes glinting. "That's no way to talk to your mother."

"But you're not my mother."

"True. Are you going to tell me where your sister is?"

"Nope."

"Naughty girl." She smiles, pulling off her black leather gloves. "I suppose I'll have to teach you a lesson."

**Book of Days ends.  
Play Chowa Oto- Kokia**

She ran at me, knife in her hand. I dodged, returning with a roundhouse kick in the stomach. She doubled over, and drew her gun.

Now I had to dodge the barrage of bullets, at least until I could draw one of my own knives. I threw it at her, knocking the gun out of her hand and pinning it to the wall.

Weapons lost, we only had our bodies. Kicks, scratches, punches, we tumbled and rolled. She had me in a choke-hold, which I barely escaped from.

Within fifteen minutes, we were both bruised and bleeding in multiple areas. I was wearing down. I stood, barely upright, breathing heavily.

Kyomi sensed my weakness. She moved in for the final blow. I stepped back-

And fell through a doorway that suddenly opened in the wall. Ran pulled her staff out of the slot next to it, and the doorway closed.

I looked around. I was in an immense cavern with a ceiling that almost looked like it was made of glass. In the center was what had once been a huge lake, but now was half-way gone. The Mirror Pool.

* * *

**Please read and review!**


	20. Decisions

**This chapter was what inspired the future sequel, I've been working on it for a while.**

**I don't own Detective Conan.**

* * *

**Play Ai no Melody- Kokia  
****_Hotaru's POV_**

In order to save Kaito, we had to put him in the Mirror Pool. The water would heal him, but it would take time.

Ran and I left our staffs by the water's edge, and carried Kaito to the center of the pool. The water was enchanted to prevent anything from sinking below the surface.

We set Kaito on the water's surface. In an instant he returned to his teenage self.

"What the-?" Ran whispered.

"The water undoes any damage done to the body," I said. "It makes sense."

Ran went to get our staffs. While she was gone, Kaito opened his eyes. He saw me.

"Hey, Hotaru-chan. Where am I?"

I knelt next to him. "You were given a very bad poison. We're here to save you."

"Oh. Okay. That explains why I feel like crap."

"Shhh. Don't talk."

In the heat of the moment, I leaned over and kissed him. He kissed back, and didn't stop until Ran came back. I almost didn't want it to end.

I stood, staff in hand. Kaito closed his eyes.

"In the deep, you shall lay, within the healing that comes with sleep," Ran and I chanted, using our staffs to coccoon Kaito in the water. He sank below the surfce, protected until the Pool could fully heal him.

We heard a banging. Someone was trying to break through the secret door. Tsukiya and Chiyoye were using magic to hold them back. "We can't keep this up much longer!"

"They'll always come back," I said. "We can't keep them away forever."

"If only this hadn't happened," Amaterasu moaned.

"It won't," Kaji said. "Because we'll create a Rift."

* * *

**Please read and review!**


	21. Rift

**I don't own Detective Conan**

* * *

**Play Requiem for a Dream  
_Tsukiya's POV_**

"What's a Rift?"

"A Rift is a change in the past to prevent an event in the present," Hotraru explained. "Creating one will take all seven mages."

We walked to the center of the pool. We stood in a cirlce, hand in hand.

"Repeat after me and Kaji-neechan," Hotaru instructed.

_Change the past, protect the present, preserve the future._

We chanted the spell without pause. Wind whipped around the cavern as a ball-like force field surrounded us, lifting us high into the air.

The Organization burst into the room.

The world went black. I was alone.

The ground crumbled below me and I fell.

* * *

**_Amaterasu's POV_**

I opened my eyes. I was sitting next to Chiyoye and Tsukiya in a small, dimly-lit room. Kaji and Hotaru were opposite us.

"Where are we?"

Kaji looked at us. "The Rift is similar to an incredibly invasive surgery," she explained. "We are simply waiting for the last 'stictches' to dissolve."

Hotaru looked at the wall. "The Rift has already made some unforseen changes."

"Like what?" Tsukiya asked.

"For one thousand years no one has been able to use magic outside the Hall of Origins," Kaji said. "Now it can be used anywhere,"

Hotaru nodded. "The Hall also contains the gate to a realm that protects magical creatures, and prevents some dangerous ones from escaping, which the Rift broke."

"Not good."

Kaji shook her head. "But we also have another issue: Ran-chan and Ao-chan shouldn't remember the events that caused the Rift, or that there even was one, just like everone else. However, they are both mages. We _need _them to re-discover the truth about themselves. Amaterasu-chan, I need you to keep an eye on Ran-chan. When she's ready, you'll bring her back to the Hall. Hotaru-chan will be keeping an eye on Ao-chan, and someone else."

"Who?" Chiyoye asked.

Kaji sighed. "Kaito-kun is still sleeping in the Mirror Pool. As a result, a Copy created to serve as a vessel for his spirit. When Kaito-kun's body has healed his Copy will need to join with him to allow him to wake up."

"What about me and Chiyoye-han?" Tsukiya asked.

"Chiyoye-chan and I will be handling the situation in the magical realm," Kaji replied. "I need _you _to keep an eye on Conan-kun."

"Why?"

"Both the Organization and Pheonix want the twins for some unknown reason," Hotaru explained. "If Conan-kun learns the truth, both groups are more likely to find out as well. The less he knows, the better."

Tsukiya nodded. "What do I need to do?"

Kaji handed him a small blue vial.

* * *

**Please read and review!**


	22. Epilogue

**I don't own Detective Conan**

* * *

**Play Kaze Ni Naru- Tsuji Ayano  
_Ran's POV_**

I opened my eyes.

"So, how is it?" Sonoko laughed.

I smiled. "It's just as good as you said it was."

"See, I knew you'd like it!"

We stood. Sonoko and I were meeting Makoto and Shinichi at the mall. Shinichi was back, so he suggested we spend the day together.

We walked by a cafe. A teenage girl and a first-grade boy were sitting at one of the tables. They looked like a ligh-haired version of me and Conan.

The girl noticed me. Our eyes met and she smiled. The girl looked strangely familiar...

"What are you looking at?" Sonoko asked.

"Nothing." I looked back at the table.

The pair had vanished.

Sonoko noticed that I wasn't beside her any more. She walked back and grabbed my arm. "Come on, they're waiting for us!"

* * *

**THE END**


	23. Author's note

**Sakura: Is it really the end?!**

**AikoTsuki: Not really, it's just the end of this part of the story. There's much more to come, trust me.**

**Ran: YAY!**

**Kaito: Am I going to wake up?**

**AikoTsuki:...**


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